TMED1 (transmembrane p24 trafficking protein 1) - Rat Genome Database
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Gene: TMED1 (transmembrane p24 trafficking protein 1) Homo sapiens
Analyze
Symbol: TMED1
Name: transmembrane p24 trafficking protein 1
RGD ID: 1354453
HGNC Page HGNC
Description: Predicted to have signaling receptor binding activity. Predicted to be involved in Golgi organization; endoplasmic reticulum to Golgi vesicle-mediated transport; and intracellular protein transport. Localizes to Golgi apparatus; endoplasmic reticulum; and endoplasmic reticulum-Golgi intermediate compartment.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: IL1RL1-binding protein; Il1rl1l; IL1RL1LG; interleukin 1 receptor-like 1 ligand; interleukin-1 receptor-like 1 ligand; MGC1270; p24 family protein gamma-1; p24g1; p24gamma1; putative T1/ST2 receptor-binding protein; ST2L; T1/ST2 receptor binding protein; Tp24; transmembrane emp24 domain containing 1; transmembrane emp24 domain-containing protein 1; transmembrane emp24 protein transport domain containing 1
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1910,832,067 - 10,836,318 (-)EnsemblGRCh38hg38GRCh38
GRCh381910,832,067 - 10,836,212 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371910,942,743 - 10,946,888 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361910,804,114 - 10,807,983 (-)NCBINCBI36hg18NCBI36
Build 341910,804,114 - 10,807,983NCBI
Celera1910,837,959 - 10,841,828 (-)NCBI
Cytogenetic Map19p13.2NCBI
HuRef1910,520,875 - 10,525,115 (-)NCBIHuRef
CHM1_11910,943,980 - 10,948,220 (-)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Molecular Function

References

Additional References at PubMed
PMID:8621446   PMID:9472029   PMID:11466339   PMID:12237308   PMID:12477932   PMID:15057824   PMID:15231748   PMID:15489334   PMID:18976975   PMID:21873635   PMID:23246001   PMID:23319592  
PMID:25609649   PMID:26186194   PMID:26496610   PMID:26972000   PMID:27173435   PMID:27432908   PMID:28298427   PMID:28380382   PMID:28514442   PMID:28675297   PMID:30833792   PMID:30862715  
PMID:31586073   PMID:31980649  


Genomics

Comparative Map Data
TMED1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1910,832,067 - 10,836,318 (-)EnsemblGRCh38hg38GRCh38
GRCh381910,832,067 - 10,836,212 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371910,942,743 - 10,946,888 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361910,804,114 - 10,807,983 (-)NCBINCBI36hg18NCBI36
Build 341910,804,114 - 10,807,983NCBI
Celera1910,837,959 - 10,841,828 (-)NCBI
Cytogenetic Map19p13.2NCBI
HuRef1910,520,875 - 10,525,115 (-)NCBIHuRef
CHM1_11910,943,980 - 10,948,220 (-)NCBICHM1_1
Tmed1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39921,418,676 - 21,421,530 (-)NCBIGRCm39mm39
GRCm39 Ensembl921,418,849 - 21,421,548 (-)Ensembl
GRCm38921,507,380 - 21,510,234 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl921,507,553 - 21,510,252 (-)EnsemblGRCm38mm10GRCm38
MGSCv37921,311,824 - 21,314,630 (-)NCBIGRCm37mm9NCBIm37
MGSCv36921,257,782 - 21,260,588 (-)NCBImm8
Celera918,775,983 - 18,778,789 (-)NCBICelera
Cytogenetic Map9A3NCBI
Tmed1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2820,059,937 - 20,063,567 (-)NCBI
Rnor_6.0 Ensembl822,540,424 - 22,542,997 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0822,540,422 - 22,544,369 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0822,594,533 - 22,598,482 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4820,611,139 - 20,613,714 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1820,611,139 - 20,613,714 (-)NCBI
Celera821,451,162 - 21,453,737 (-)NCBICelera
Cytogenetic Map8q13NCBI
Tmed1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554951,934,920 - 1,938,208 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554951,934,920 - 1,938,208 (-)NCBIChiLan1.0ChiLan1.0
TMED1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11911,107,511 - 11,111,744 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1911,107,511 - 11,111,744 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01910,386,041 - 10,389,905 (-)NCBIMhudiblu_PPA_v0panPan3
TMED1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12050,395,862 - 50,399,118 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2050,396,005 - 50,407,535 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2050,268,438 - 50,280,141 (+)NCBI
ROS_Cfam_1.02050,917,471 - 50,929,210 (+)NCBI
UMICH_Zoey_3.12050,126,288 - 50,137,982 (+)NCBI
UNSW_CanFamBas_1.02050,553,831 - 50,565,514 (+)NCBI
UU_Cfam_GSD_1.02050,795,278 - 50,806,997 (+)NCBI
Tmed1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118209,305,083 - 209,308,562 (+)NCBI
SpeTri2.0NW_0049366591,046,144 - 1,049,628 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TMED1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl269,568,354 - 69,576,066 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1269,573,128 - 69,576,421 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2270,006,707 - 70,009,745 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TMED1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.169,829,529 - 9,833,559 (-)NCBI
ChlSab1.1 Ensembl69,830,086 - 9,833,529 (-)Ensembl
Tmed1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248282,805,015 - 2,808,232 (-)NCBI

Position Markers
IL1RL1LG_155  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371910,943,061 - 10,943,786UniSTSGRCh37
Build 361910,804,061 - 10,804,786RGDNCBI36
Celera1910,837,906 - 10,838,631RGD
HuRef1910,521,193 - 10,521,918UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:2123
Count of miRNA genes:667
Interacting mature miRNAs:769
Transcripts:ENST00000214869, ENST00000586835, ENST00000588259, ENST00000588289, ENST00000589638, ENST00000591157, ENST00000591695
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High
Medium 2402 2817 1643 547 1615 390 4349 2099 3061 400 1429 1601 170 1204 2786 4
Low 37 174 83 77 336 75 7 98 673 18 31 12 4 1 2 2 2
Below cutoff 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000214869   ⟹   ENSP00000214869
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1910,832,067 - 10,836,212 (-)Ensembl
RefSeq Acc Id: ENST00000586835   ⟹   ENSP00000464856
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1910,832,687 - 10,835,004 (-)Ensembl
RefSeq Acc Id: ENST00000588259   ⟹   ENSP00000468054
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1910,832,975 - 10,836,201 (-)Ensembl
RefSeq Acc Id: ENST00000588289   ⟹   ENSP00000464824
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1910,832,985 - 10,835,632 (-)Ensembl
RefSeq Acc Id: ENST00000589638   ⟹   ENSP00000467690
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1910,833,051 - 10,836,195 (-)Ensembl
RefSeq Acc Id: ENST00000591157   ⟹   ENSP00000468492
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1910,832,985 - 10,836,249 (-)Ensembl
RefSeq Acc Id: ENST00000591695   ⟹   ENSP00000468294
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1910,832,813 - 10,836,318 (-)Ensembl
RefSeq Acc Id: NM_006858   ⟹   NP_006849
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381910,832,067 - 10,836,212 (-)NCBI
GRCh371910,942,743 - 10,946,983 (-)NCBI
Build 361910,804,114 - 10,807,983 (-)NCBI Archive
Celera1910,837,959 - 10,841,828 (-)RGD
HuRef1910,520,875 - 10,525,115 (-)NCBI
CHM1_11910,943,980 - 10,948,220 (-)NCBI
Sequence:
RefSeq Acc Id: NR_104015
RefSeq Status: REVIEWED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381910,832,067 - 10,835,740 (-)NCBI
HuRef1910,520,875 - 10,525,115 (-)NCBI
CHM1_11910,943,980 - 10,947,652 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006722631   ⟹   XP_006722694
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381910,832,438 - 10,835,591 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_006849   ⟸   NM_006858
- Peptide Label: precursor
- UniProtKB: Q13445 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006722694   ⟸   XM_006722631
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSP00000214869   ⟸   ENST00000214869
RefSeq Acc Id: ENSP00000464856   ⟸   ENST00000586835
RefSeq Acc Id: ENSP00000464824   ⟸   ENST00000588289
RefSeq Acc Id: ENSP00000468054   ⟸   ENST00000588259
RefSeq Acc Id: ENSP00000467690   ⟸   ENST00000589638
RefSeq Acc Id: ENSP00000468294   ⟸   ENST00000591695
RefSeq Acc Id: ENSP00000468492   ⟸   ENST00000591157
Protein Domains
GOLD

Promoters
RGD ID:6811794
Promoter ID:HG_ACW:39890
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:K562
Transcripts:TMED1.CAPR07
Position:
Human AssemblyChrPosition (strand)Source
Build 361910,806,856 - 10,807,356 (-)MPROMDB
RGD ID:6796112
Promoter ID:HG_KWN:28882
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   CD4+TCell_2Hour,   HeLa_S3,   Jurkat,   K562,   Lymphoblastoid,   NB4
Transcripts:NM_006858
Position:
Human AssemblyChrPosition (strand)Source
Build 361910,807,726 - 10,808,422 (-)MPROMDB
RGD ID:7238543
Promoter ID:EPDNEW_H25015
Type:multiple initiation site
Name:TMED1_1
Description:transmembrane p24 trafficking protein 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381910,836,210 - 10,836,270EPDNEW

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 19p13.2-13.13(chr19:8831147-13331227)x3 copy number gain See cases [RCV000052908] Chr19:8831147..13331227 [GRCh38]
Chr19:8941823..13442041 [GRCh37]
Chr19:8802823..13303041 [NCBI36]
Chr19:19p13.2-13.13
likely pathogenic
GRCh38/hg38 19p13.2-13.12(chr19:10315258-14048994)x3 copy number gain See cases [RCV000052909] Chr19:10315258..14048994 [GRCh38]
Chr19:10425934..14159806 [GRCh37]
Chr19:10286934..14020806 [NCBI36]
Chr19:19p13.2-13.12
pathogenic
NM_001005360.2(DNM2):c.2515C>T (p.Pro839Ser) single nucleotide variant Malignant melanoma [RCV000063422] Chr19:10830350 [GRCh38]
Chr19:10941026 [GRCh37]
Chr19:10802026 [NCBI36]
Chr19:19p13.2
not provided
GRCh38/hg38 19p13.2(chr19:9735443-11228001)x1 copy number loss See cases [RCV000135403] Chr19:9735443..11228001 [GRCh38]
Chr19:9846119..11338677 [GRCh37]
Chr19:9707119..11199677 [NCBI36]
Chr19:19p13.2
pathogenic
GRCh38/hg38 19p13.2(chr19:10156406-10889688)x3 copy number gain See cases [RCV000136738] Chr19:10156406..10889688 [GRCh38]
Chr19:10267082..11000364 [GRCh37]
Chr19:10128082..10861364 [NCBI36]
Chr19:19p13.2
pathogenic
GRCh38/hg38 19p13.2(chr19:10330655-10920552)x1 copy number loss See cases [RCV000141708] Chr19:10330655..10920552 [GRCh38]
Chr19:10441331..11031228 [GRCh37]
Chr19:10302331..10892228 [NCBI36]
Chr19:19p13.2
likely pathogenic
GRCh38/hg38 19p13.2-13.13(chr19:10319474-13777860)x1 copy number loss See cases [RCV000141568] Chr19:10319474..13777860 [GRCh38]
Chr19:10430150..13888674 [GRCh37]
Chr19:10291150..13749674 [NCBI36]
Chr19:19p13.2-13.13
pathogenic
GRCh37/hg19 19p13.2-13.12(chr19:9678768-14853426) copy number gain See cases [RCV000446985] Chr19:9678768..14853426 [GRCh37]
Chr19:19p13.2-13.12
pathogenic
GRCh37/hg19 19p13.2(chr19:10286133-11040457)x1 copy number loss See cases [RCV000446752] Chr19:10286133..11040457 [GRCh37]
Chr19:19p13.2
pathogenic
GRCh37/hg19 19p13.3-q13.43(chr19:260912-58956888) copy number gain See cases [RCV000512296] Chr19:260912..58956888 [GRCh37]
Chr19:19p13.3-q13.43
pathogenic
GRCh37/hg19 19p13.3-q13.43(chr19:260912-58956888)x3 copy number gain See cases [RCV000511289] Chr19:260912..58956888 [GRCh37]
Chr19:19p13.3-q13.43
pathogenic|uncertain significance
GRCh37/hg19 19p13.3-q13.43(chr19:260912-59097160)x3 copy number gain not provided [RCV000752444] Chr19:260912..59097160 [GRCh37]
Chr19:19p13.3-q13.43
pathogenic
GRCh37/hg19 19p13.3-q13.43(chr19:68029-59110290)x3 copy number gain not provided [RCV000752439] Chr19:68029..59110290 [GRCh37]
Chr19:19p13.3-q13.43
pathogenic
Single allele deletion not provided [RCV000844961] Chr19:10642984..12810067 [GRCh37]
Chr19:19p13.2
not provided
GRCh37/hg19 19p13.2(chr19:10441330-10977962)x1 copy number loss not provided [RCV000849141] Chr19:10441330..10977962 [GRCh37]
Chr19:19p13.2
uncertain significance
GRCh37/hg19 19p13.2(chr19:10642984-12810067) copy number loss not provided [RCV001249213] Chr19:10642984..12810067 [GRCh37]
Chr19:19p13.2
not provided
GRCh37/hg19 19p13.2(chr19:10632623-11135294)x3 copy number gain not provided [RCV001007031] Chr19:10632623..11135294 [GRCh37]
Chr19:19p13.2
uncertain significance
NC_000019.9:g.(?_10912954)_(11200309_?)dup duplication Familial hypercholesterolemia [RCV001345083] Chr19:10912954..11200309 [GRCh37]
Chr19:19p13.2
uncertain significance

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:17291 AgrOrtholog
COSMIC TMED1 COSMIC
Ensembl Genes ENSG00000099203 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSP00000214869 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000464824 UniProtKB/TrEMBL
  ENSP00000464856 UniProtKB/TrEMBL
  ENSP00000467690 UniProtKB/TrEMBL
  ENSP00000468054 UniProtKB/TrEMBL
  ENSP00000468294 UniProtKB/TrEMBL
  ENSP00000468492 UniProtKB/TrEMBL
Ensembl Transcript ENST00000214869 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000586835 UniProtKB/TrEMBL
  ENST00000588259 UniProtKB/TrEMBL
  ENST00000588289 UniProtKB/TrEMBL
  ENST00000589638 UniProtKB/TrEMBL
  ENST00000591157 UniProtKB/TrEMBL
  ENST00000591695 UniProtKB/TrEMBL
GTEx ENSG00000099203 GTEx
HGNC ID HGNC:17291 ENTREZGENE
Human Proteome Map TMED1 Human Proteome Map
InterPro GOLD_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GOLD_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TMP21-related UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:11018 UniProtKB/Swiss-Prot
NCBI Gene 11018 ENTREZGENE
OMIM 605395 OMIM
PANTHER PTHR22811 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam EMP24_GP25L UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA134972147 PharmGKB
PROSITE GOLD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART EMP24_GP25L UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF101576 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt K7EIN4_HUMAN UniProtKB/TrEMBL
  K7EIR1_HUMAN UniProtKB/TrEMBL
  K7EQ63_HUMAN UniProtKB/TrEMBL
  K7ER03_HUMAN UniProtKB/TrEMBL
  K7ERK5_HUMAN UniProtKB/TrEMBL
  K7ES06_HUMAN UniProtKB/TrEMBL
  Q13445 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-08-18 TMED1  transmembrane p24 trafficking protein 1  TMED1  transmembrane emp24 protein transport domain containing 1  Symbol and/or name change 5135510 APPROVED